Hi, please help me in resolving the following error
Error in checkIDs(genes, metabolites) :
The following IDs were not found in the keylist and thus are not able to be converted:
ENTREZID: 58003, 797319, 561370, 567205, 570167, 560802...
This error I got when using obtainedgelist for daniorerio entrezid from kegg and reactome.
Hi, welcome!
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AnnotationDbi::keytypes(org.Dr.eg.db::org.Dr.eg.db)
#>
#> [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
#> [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
#> [11] "GO" "GOALL" "IPI" "ONTOLOGY" "ONTOLOGYALL"
#> [16] "PATH" "PFAM" "PMID" "PROSITE" "REFSEQ"
#> [21] "SYMBOL" "UNIPROT" "ZFIN"
head(rownames(Y))
#> Error in rownames(Y): object 'Y' not found
table(group1)
#> Error in table(group1): object 'group1' not found
paths <- graphite::pathways('drerio','kegg')
paths[[1]]
#> "Glycolysis / Gluconeogenesis" pathway
#> Native ID = dre:00010
#> Database = KEGG
#> Species = drerio
#> Number of nodes = 107
#> Number of edges = 1619
#> Retrieved on = 22-04-2022
#> URL = http://www.kegg.jp/kegg-bin/show_pathway?org_name=dre&mapno=00010
head(nodes(paths[[1]]))
#> Error in nodes(paths[[1]]): could not find function "nodes"
pathways_mat[1:5,7, drop = FALSE]
#> Error in eval(expr, envir, enclos): object 'pathways_mat' not found
library(netgsa)
database_search <- obtainEdgeList(rownames(Y),c("kegg","reactome"))
#> Error in rownames(Y): object 'Y' not found
Created on 2022-08-29 by the reprex package (v2.0.1)
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